Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012010.1 Kokia drynarioides strain JFW-HI SEQ_127008, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 1789
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38


Found at i:744 original size:37 final size:38

Alignment explanation


    Indices: 694--774  Score: 92
    Period size: 37  Copynumber: 2.2  Consensus size: 38

        684 TTCGAAGCAA

                            **        *           
        694 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
          1 TAAAGTGACACCCAGTACCTCATCGTACCTAGCCGAAG

                   **                  *   *      
        731 TAAAGTGGTACCCAGTACCTCATCGTATCTATCCGAAG
          1 TAAAGTGACACCCAGTACCTCATCGTACCTAGCCGAAG

                  
        769 TAAAGT
          1 TAAAGT

        775 AATGACACCC


Statistics
Matches: 36,  Mismatches: 7, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  37   21  0.58
  38   15  0.42

ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23


Consensus pattern (38 bp):   
TAAAGTGACACCCAGTACCTCATCGTACCTAGCCGAAG

Found at i:1621 original size:8 final size:9

Alignment explanation


    Indices: 1600--1641  Score: 50
    Period size: 9  Copynumber: 4.6  Consensus size: 9

       1590 CTGTTCTTCC

                     
       1600 TTCTTTTAT
          1 TTCTTTTAT

                     
       1609 TTCTTTT-T
          1 TTCTTTTAT

                    * 
       1617 TTCTTTCTTT
          1 TTCTTT-TAT

                      
       1627 ATTCTTTTAT
          1 -TTCTTTTAT

                 
       1637 TTCTT
          1 TTCTT

       1642 ATATATATAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 6
        0.81            0.03        0.17

Matches are distributed among these distances:
   8    7  0.24
   9   13  0.45
  10    3  0.10
  11    6  0.21

ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79


Consensus pattern (9 bp):   
TTCTTTTAT

Found at i:1629 original size:20 final size:20

Alignment explanation


    Indices: 1604--1641  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1594 TCTTCCTTCT

                                 
       1604 TTTATTTCTTTT-TTTCTTTC
          1 TTTA-TTCTTTTATTTCTTTC

                              
       1624 TTTATTCTTTTATTTCTT
          1 TTTATTCTTTTATTTCTT

       1642 ATATATATAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  19    7  0.41
  20   10  0.59

ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79


Consensus pattern (20 bp):   
TTTATTCTTTTATTTCTTTC
Done.